What breed is she? Some thick-feathered chickens have such thick feathers, you need to trim some feathers away from her vent area to give the rooster a better target. Sometimes it is the rooster that needs trimming. This does not happen to each and every chicken in these breeds (it's not really that common), but Orpingtons and Cochin are two breeds where this occasionally happens.

Some hens resist the rooster's advances a lot more than others. Does she cooperate when he tries with her?

Practically all of a hens mating and brooding behaviors are instinctive. Almost all hens get it right, which to me is pretty remarkable. But occasionally a hen does not get it quite right.

The hen's internal egg laying factory is a bit complex. A lot of things have to happen right to get fertile eggs. Again, it is remarkable that so many of them get it right, but occasionally there is one that just does not get it right.

An older hen can lose fertility, just like a rooster. The internal quality of her eggs can change too. If she is four or five years old, she may just not be laying fertile eggs any more.

I'm sure there are other possible reasons. It sure sounds like something to do with the individual hen.

Ridgerunner is right about it maybe being the breed or the fact that the hen doesn't cooperate. My biggest, favorite black orp hen hardly ever lays fertile eggs. And it's not about the fluffy butt, it's because she wiggles and jostles around while he's trying to do this job. But there are those breeders who don't get many fertile eggs until they trim or pull the feathers around their vents. I've done it but it didnt' improve fertility for me. Which is amazing, considering the fluff around there. Those Orps have so much fluff that it takes some time just to find the vent!